Skip to content

FastK: Segmentation fault with small data #22

@junaruga

Description

@junaruga

Hello,
On the latest master f18a4e6 , I was trying to test the FastK with a small test data. Then I got the following Segmentation fault. Do you have any idea about how to fix it? Thank you.

$ pwd
/home/jaruga/git/FASTK

$ gcc --version
gcc (GCC) 12.2.1 20220819 (Red Hat 12.2.1-1)
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ make
$ cat fastk_source.fasta 
>FastK input source
ACTG
$ ./FastK -v fastk_source.fasta 

Partitioning 1 .fasta file into 4 parts
  File is so small will use only 1 thread 

Determining minimizer scheme & partition for fastk_source

FastK: Warming Sequences are on average smaller than 1.5x k-mer size!
  Estimate -0.036K 40-mers
  Handling data in a single block
  Using 5-minimizers with 1024 core prefixes

Phase 1: Partitioning K-mers into 1 Super-mer Files

  There are 1 reads totalling 4 bps

     Part:  40-mer  super-mers  ave. length
        0:       0           0           NA
      Sum:       0           0           NA

      Range 0 - 0

  Resources for phase:  0.000u  0.001s  0.001w  127.8%

Phase 2: Sorting & Counting K-mers in 1 blocks

  Processing block 1: Sorting super-mers     Segmentation fault (core dumped)

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions